Yuu Kanda, from D. Gray-Man. No doubt in my mind.
He was a research specimen that died in his former life then was somehow brought back to life.
They experimented on him everyday, trying to fuse him with Innocence, and basically nearly killed him everyday(thank goodness he has high regeneration abilities).
He also remembered some of his memories from his former life that caused him to suffer.
He was also about to be 'frozen' and disposed of, as a test subjest, but Kanda's friend Alma saved him.
But then Alma got his memories back and killed everybody in the lab.
Then, Kanda was forced to kill his own best friend(Alma).

Taken from: http://paradisa.wikia.com/wiki/Kanda_Yuu#Random_Official_Stats

"Kanda was born in a hole a child of about nine-years-old in the Sixth Asia Research Facility. Nine years ago, the Order had begun a secret project to create artificial disciples to synch with the Innocence. Because a normal human's body cannot handle the rejection of Innocence and would die, the Order created artificial test bodies with the ability to regenerate all wounds. Two bodies were successful, Kanda Yuu and Alma Karma. As soon as Kanda was born, he was forced to synch with Innocence, killing him multiple times every session. After death, it would take about ten minutes to regenerate before the next attempt would begin. Kanda sort of hated the Innocence and the world he was born into and sort of just wanted to go back to sleep in his little hole. He also began hallucinating a strange woman in the mist in the cold room he was born. Concepts like "mother" and "father" were foreign to him, because he never had them.

In reality, Kanda did have parents... but in another life. The truth behind the second exorcist project? Kanda was an exorcist who died on the battle field, but whose body was collected by the Order and whose brain was then implanted into an artificial body, a child. His memories were wiped clean, his real body was mummified and fixed to his Innocence -- the one Kanda was forced to synch with. The test was to see if it was possible to continue synchro even after death. Kanda's "hallucinations" were in fact memories of his past life, the woman was a person from his life before he was "Yuu". When it was discovered that Kanda was regaining his memories, he was slated to be disposed of. Just as he realized, overcome with anger, the true nature of the project, the Order "put him down" by sending him into a permanent coma. Assaulted by his past memories even in a coma, Kanda's Innocence appears before him, waking him from his sleep. He uses his Innocence to escape.

More so, Kanda met Alma, the other test subject. Alma was bright, happy, always wanting to please and make friends. Kanda hated him passionately and couldn't understand how Alma could laugh when their world was so utterly horrible. Alma stalked Kanda relentlessly and eventually Kanda understood Alma's POV a bit better, laughing along with him after both them were a mess after their synchro session. They became friends, but Alma, trying to save Kanda from disposal, synched with an Innocence, killed a few members of the ninja-like group Crow, and discovered their real bodies. Losing his mind (?), Alma massacred the entire lab, killing 46 personnel. Kanda, the only survivor, was forced to hack Alma to pieces until he stopped regenerating. Kanda was under the impression he had killed Alma. "

well i aven't watched any of the animes mentioned except for naruto and maybe more XD it's just i can't be bothered going through the 144 pages XD but the anime i watched had a childhood of this girl and she lived in this rich family but then one day her parents went someplace i forgot XD but it was only her and her 2 younger sisters and 1 youngest brother at home, so then burglars came and decided to rob them but they couldn't find any money so they told the oldest sister which is her to bring them money cause she's the oldest and her parents would of told her where it was but she really didn't know and she told them that but they didn't believe her so they decided to threaten her to bring it, threatening her by taking her 3 siblings and saying that they will shoot them one by one every 10 minutes, so she ran all over the house looking for money but she found out she was running out of time so she decided to just give them a big vase she found, she had trouble carrying it because it was heavy but like she did anyways, then as she was getting down the stairs so close to them she slipped and broke it and then it was too late.......the police then arrived 30 minutes later and there was blood splattered all over the wall.........to me that is really rough and sad T.T soo yeah that's the worst childhood to mee XD hope someone read this at least T.T

This is from a manga, but since it was particularly memorable in my opionion as far as the extent of the realism is concerned, so I'll still go with it:

Rei Kiriyama from Sangatsu no Lion - Spoiler-heavy, if you're particularly annoyed at those kind of thing.

Spoiler Alert! Click to show or hide

-Rei played Shogi under the influence of his father and his friend, because he couldn't communicate properly with his friends. He wasn't good at it nor enjoyed it, but worked hard to play it since it was the only time he could spend with his father.

-One day, his father, mother and younger sister all die due to a car crash as they were returning from their trip. His relatives, who were only interested in his father's hospital decides to put him into an institution. During his family's funeral, his father's friend comes into his room, asking if he likes shogi. In order to avoid being sent to the institution, he lies that he likes shogi, permanently binding his life with the 'god of shogi' and his family.

-Even after when he arrived at his new home, he was constantly reminded that it was not his true family by the aggressive stepsister Kyoko and depressed stepbrother Ayumu . He feels more guilt as his stepfather decides that his children will have to forfeit their dreams in becoming shogi professionals as they have unable to reach a certain rank within the period of time.

-Pressured by his stepfather's support, Rei and his 'siblings' separated their ways, as he absorbed himself more into the world of professional shogi, while Kyoko spent her times outside and Ayumu locking himself inside and drowning in games.

-Fearing that his existence will eventually consume his foster family, Rei decides to drop out of school to concentrate on shogi, earning his own income by becoming a shogi professional and leave the household as soon as possible.

-The relationship between Rei and Kyoko is very complex: Kyoko shows genuine hatred him for taking away the attention of her father away from her, but there's clearly an aspect of love (romantically or fraternally depending on interpretations) between each other as they grow up and mature, hinted as her frequent reference and the fact that he hates the shogi legend whom Kyoko used to be obsessed about; he goes into a rage for the first time and tries to punch him when he made insults about her.
Possibly one of the saddest page of the volume.

For a manga that has only 4 total published volumes / 15 scanlated chapters, Sangatsu no Lion has one of the most realistic, complex and tragic childhood I've ever seen in an anime and manga. The good thing about this is, that it has so much more potential to be followed. If you are a fan of Umino Chika's works (Honey & Clover), or enjoy one of the most realistic tragic slice-of-life, I'd definitely recommend this series, even if the updates are rather slow. It is truly a series with a rather unique atmosphere which distinctively sets it apart from the rest of the slice-of-life counterparts.

Ciel Phantomhive from Kuroshitsuji..his family murdered-he is a noble-..he was kidnapped on his tenth birthdayHis kidnappers then sold him.branded a mark of his slavery on his back, and later used him as a sacrifice.
Then he exchanged his soul to a demon in return for help with revenge .
Then he came back as the head of the Phantomhive's fam. and his job is as the Queen's watchdog.Doin evrything the Queen's ask him to do -evil things,something like that-